Since I don't have the correct tools to measure my deck that I wanted as close to zero as possible. When I drop the block at the machine shop I told him I wanted the block zero deck but did not install the pistons and take measurement. he just use the rod length, centerline and actual deck height to get it close to zero. I tried to measure with a straight edge to verify the true height and get different reading depending on where I measure on the piston. The pistons are Wiseco Flattop Pro-Tru 5.4cc.
1. Above the valve relief eyebrow I cannot get a .002 feeler guage between the straight edge and piston.
2. Below the the valve relief I got about .003
3. Close to the bottom of the pistons I get .005

Where are suppose to measure deck height?

You should try to measure in the middle because of piston rock.
You could also measure towards the top or bottom & rock the piston & average the two readings.

I do it right over the pin.

DB,
Unless you have a way to measure crankshaft stroke, rod length, and piston compression height ... you really need to assemble the engine to get it right. Crank stroke is the biggest variable. I have seen stock cranks easily vary .005" in stroke. Some aftermarket ones are not much better. If you really want "0" deck, do it right and assemble it or pay your machine shop to do it.
Just my opinion,

And your rods may not be exactly the same length, either, especially if they're stock.